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Detailed information for vg1124477987:

Variant ID: vg1124477987 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24477987
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCTAGAATCTTCGCCACTGCATTAGTGCTCTTCCACGGCACCGGCTCCGGTGGCACCTCCTGGCCGCCAGCGCCGCCGCAGCATTGGGCGTTCTTCCAC[C/A]
CTATTCCTTGATCCGTCGTCGCCGTCGATTAACTGCTAATTACTCTGAGCGGTGCCGACCAACATGGAGGGATGAAGCCGTAAATCTATGTATCGTCAGA

Reverse complement sequence

TCTGACGATACATAGATTTACGGCTTCATCCCTCCATGTTGGTCGGCACCGCTCAGAGTAATTAGCAGTTAATCGACGGCGACGACGGATCAAGGAATAG[G/T]
GTGGAAGAACGCCCAATGCTGCGGCGGCGCTGGCGGCCAGGAGGTGCCACCGGAGCCGGTGCCGTGGAAGAGCACTAATGCAGTGGCGAAGATTCTAGGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 33.60% 2.50% 8.44% 55.44% NA
All Indica  2759 39.30% 0.00% 10.15% 50.49% NA
All Japonica  1512 21.90% 7.30% 3.44% 67.33% NA
Aus  269 42.40% 0.40% 19.70% 37.55% NA
Indica I  595 31.30% 0.00% 15.29% 53.45% NA
Indica II  465 24.10% 0.00% 7.31% 68.60% NA
Indica III  913 49.30% 0.00% 9.31% 41.40% NA
Indica Intermediate  786 42.90% 0.10% 8.91% 48.09% NA
Temperate Japonica  767 32.30% 0.00% 1.96% 65.71% NA
Tropical Japonica  504 10.10% 20.80% 4.37% 64.68% NA
Japonica Intermediate  241 13.30% 2.50% 6.22% 78.01% NA
VI/Aromatic  96 29.20% 2.10% 6.25% 62.50% NA
Intermediate  90 34.40% 3.30% 8.89% 53.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1124477987 C -> A LOC_Os11g40890.1 intron_variant ; MODIFIER silent_mutation Average:4.476; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1124477987 C -> DEL N N silent_mutation Average:4.476; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124477987 NA 9.78E-06 mr1039 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124477987 NA 5.55E-06 mr1083 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124477987 2.17E-06 2.17E-06 mr1266 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124477987 NA 1.14E-06 mr1345 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124477987 NA 1.16E-06 mr1427 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124477987 NA 4.75E-06 mr1560 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124477987 NA 1.27E-06 mr1700 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124477987 8.73E-06 9.51E-06 mr1707 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124477987 1.28E-07 5.83E-10 mr1852 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251